How do we match up ITIL V3 and ISO 20000. What I read about ISO 20000, it was aligned to ITIL V2. Now that we have V3 in place how are we aligning both of them? Or is there some other refresh for ISO coming in too?

That said, I cannot see any reason to worry about things. If you want to be certified to the standard, then you design systems, using ITIL guidance, to meet the standard. The apparently close relationship is irrelevant and it would be illogical to expect it to remain so close as the developmental directions of the two are very different.

If I were building a service management system (and I will as soon as someone asks me to), I would use the standard as my ruler (whether I was going for certification or not) and ITIL as a collection of crayons for drawing the line._________________"Method goes far to prevent trouble in business: for it makes the task easy, hinders confusion, saves abundance of time, and instructs those that have business depending, both what to do and what to hope."
William Penn 1644-1718